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We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…
The effect of mutations on protein structures is usually rather localized and minor. Finding a mutation that can single-handedly change the fold and/or topology of a protein structure is a rare exception. The A31P mutant of the homodimeric…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
How do protein structure prediction models fold proteins? We investigate this question by tracing how ESMFold folds a beta hairpin, a prevalent structural motif. Through counterfactual interventions on model latents, we identify two…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
This work examines the conformational ensemble involved in $\beta$-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent…
Cu,Zn superoxide dismutase (SOD1) has been implicated in the familial form of the neurodegenerative disease Amyotrophic Lateral Sclerosis (ALS). It has been suggested that mutant mediated SOD1 misfolding/aggregation is an integral part of…
Protein biologics hold immense potential in therapeutic applications, but their ephemeral nature has hindered their widespread application. The effects of different stressors on protein folding have long been studied, but whether these…
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…
Superoxide dismutase-1 (SOD1) is a ubiquitous, Cu and Zn binding, free radical defense enzyme whose misfolding and aggregation play a potential key role in amyotrophic lateral sclerosis, an invariably fatal neurodegenerative disease. Over…
Viroporins are small viral proteins that oligomerize in the membrane of host cells and induce the formation of hydrophilic pores in these membranes, thus altering the physiological properties of the host cells. Due to their significance for…
Natively unstructured proteins defy the classical "one sequence-one structure" paradigm of protein science. Monomers of these proteins in pathological conditions can aggregate in the cell, a process that underlies socially relevant…
Mathematical modeling offers a valuable approach to understanding Alzheimers disease (AD) given its complexity, unknown causes, and lack of effective treatments. Models, once validated, offer a powerful tool to test medical hypotheses that…
A mutation in a protein-coding gene in DNA can alter the protein structure coded by the same gene. Structurally altered proteins usually lose their functions and sometimes gain an undesirable function instead. These types of mutations and…
Field evaporation in atom probe tomography (APT) includes known processes related to surface migration of atoms, such as the so-called roll-up mechanism. They lead to trajectory aberrations and artefacts on the detector. These processes are…
Chromosomal aberrations are very frequent in leukemias and several recurring mutations capable of malignant transformation have been described. These mutations usually occur in hematopoietic stem cells (HSC), transforming them into leukemia…
Considerable mechanistic insight has been gained into amyloid aggregation; however, a large class of non-amyloid protein aggregates are considered 'amorphous,' and in most cases little is known about their mechanisms. Amorphous aggregation…
Learning how proteins fold will hardly have any impact in the way conventional -- active site centered -- drugs are designed. On the other hand, this knowledge is proving instrumental in defining a new paradigm for the identification of…
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…